|
| Status |
Public on Jan 07, 2008 |
| Title |
Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 12). |
| Sample type |
RNA |
| |
|
| Source name |
3T3 cells from cyclin D1KO mice infected with MSCV-D1a.
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6
Age: E14
Retrovirus: MSCV-D1a
|
| Treatment protocol |
Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-D1a murine stem cell virus.
|
| Growth protocol |
Cells maintained in DMEM supplemented with 10% fetal bovine serum/ 100u/ml of Penicillin-Streptomycin and cultured at 37oC in 5% carbon dioxide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
|
| Label |
Biotin
|
| Label protocol |
Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.
|
| |
|
| Hybridization protocol |
The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.
|
| Scan protocol |
Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.
|
| Description |
Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.
|
| Data processing |
The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.
|
| |
|
| Submission date |
Sep 25, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Mathew Casimiro |
| E-mail(s) |
Matthew.Casimiro@mail.jci.tju.edu
|
| Organization name |
Thomas Jefferson University
|
| Department |
Cancer Biology
|
| Lab |
Pestell Lab
|
| Street address |
1035 BLSB, 233 South 10th street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE9161 |
Expression profiling of cyclin D1 splice variants cyclin D1a and D1b in mouse 3T3 cells. |
|
| Relations |
| Reanalyzed by |
GSE119085 |
